Combinational test of DGKi with PD-1 blocker
scTCR-seq + scRNA-seq
DGKi
- DGKs are physiological regulators of T-cell
development,differentiation, and function.
- Inhibition of DGK may restore the T-cell activation program
- Enhanced effects may be seen with combination therapy (Nivolumab + DGKi)
Data
Sample name: P*****
Condition (1 control, 3 test conditions): CONTROL, CND1, CND2,
COMBO
Number of cells : 8096 cells
Initial Processing
## perform default analysis
perform_default_analysis <- function(obj.srt, n_features = 2000, n_pcs = 20,
dims_for_neighbors = 1:10,
resolutions = c(0.2, 0.5),
umap_dims = 1:10) {
# Step 1: Find variable features
obj.srt <- FindVariableFeatures(obj.srt,
selection.method = 'vst',
nfeatures = n_features)
# Step 2: Scale and normalize data
all_genes <- rownames(obj.srt)
obj.srt <- NormalizeData(obj.srt)
obj.srt <- ScaleData(obj.srt, features = all_genes)
# Step 3: Run PCA
obj.srt <- RunPCA(obj.srt,
features = VariableFeatures(object = obj.srt), npcs = n_pcs)
# Step 4: Find neighbors
obj.srt <- FindNeighbors(obj.srt, dims = dims_for_neighbors)
# Step 5: Find clusters
obj.srt <- FindClusters(obj.srt, resolution = resolutions)
# Step 6: Run UMAP
obj.srt <- RunUMAP(obj.srt, dims = umap_dims)
# Return the Seurat object with analysis results
return(obj.srt)
}
# apply
obj.srt <- perform_default_analysis(obj.srt)Numer of cells
UMAP (sample)
Colored by condition
Colored by each condition
Clustering
UMAP colored by cluster (two resolutions)
Distribution of cells by cluster and condition (res 0.1)
TABLE : Distribution of cells by cluster and condition (res 0.1)
HEATMAP : Distribution of cells by cluster and condition (res 0.1)
Distribution of cells by cluster and condition (res 0.5)
TABLE : Distribution of cells by cluster and condition (res 0.5)
HEATMAP : Distribution of cells by cluster and condition (res 0.5)
# Clonotype Analysis
Clonotype Diversity
CTRL clonotype diversity
CND1 clonotype diversity
CND2 clonotype diversity
COMB clonotype diversity
scRepertoire
Clonotype analysis using scRepertoire
Quantify Clonotypes
Unique clonotypes by TRA chain
Unique clonotypes by TRB chain
Clonotype Abundance
Length of Clonotypes
Compare Clonotypes
Visualize Gene Usage
More Advanced Clonal Analysis
Diversity Analysis
Further Analysis (Specific cell type+clonotype)
Cytotoxic Markers and associated clonotypes
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